I didn't change the adsense code on my pages either, but after the introduction of the colour options, the code within the iframe, produced by google at runtime, has changed to always show space for 4 ads.

Before that change, the skyscrapers were indeed collapsable, showing just the number of boxes needed. Looked very nice on a contrasting background, and I was designing new changes around that look, but now the empty boxes just look silly.

Since the change is within the code they produce at runtime there's nothing we can do to alter it, which is why I asked for the option to keep it as it was. Still no reply though, must be very backlogged on adsense support.